Internal flooding in nuclear power plants is a possible internal disaster, which will lead to serious accidents in nuclear power plants, so it is necessary to evaluate for safety. CNIFA software is an advanced three-dimensional simulation software with independent intellectual property rights developed by China Nuclear Power Engineering Co., Ltd., which is specially used for internal flooding analysis of nuclear power plants. Compared with traditional flood analysis software, CNIFA has the advantages of good applicability and visualization. Interacted with E3D or PDMS software, the existing three-dimensional model of the nuclear power plant can be used directly as an input by CNIFA; the flooding scene inside the nuclear power plant can be dynamically simulated and the whole process of water flow spreading in the nuclear power plant in three dimensions can be clearly displayed by CNIFA. In this study, three -dimensional simulation software CNIFA is used to analyze the internal flooding safety of small reactor (ACP100), and some suggestions for design improvement are put forward. Firstly, the physical model of the plant (reduction ratio 1:10) is built to simulate the water flooding spread in the room of the nuclear power plant. The physical experimental results are compared with the simulation results of CNIFA. The results show that CNIFA has good applicability and accuracy in internal flooding safety assessment. Secondly, the safety assessment of the possible flooding event in ACP100 nuclear power plant is carried out through CNIFA, and the protective measures are taken for the important safety equipment in the plant according to the simulation results.